Variant report

Variant	rs2659058
Chromosome Location	chr19:51326106-51326107
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr19:51325930-51327211	K562	blood:	n/a	chr19:51327165-51327174 chr19:51327164-51327173 chr19:51327163-51327172

No.	Distal block	Cell Line	Cell type
1	chr19:51324739..51330198-chr19:51333522..51340343,9	K562	blood:
2	chr19:51324313..51327368-chr19:51329221..51331618,3	MCF-7	breast:
3	chr19:51306219..51311443-chr19:51320268..51326410,9	MCF-7	breast:
4	chr19:51317914..51322870-chr19:51325257..51328084,4	MCF-7	breast:
5	chr19:51306849..51308707-chr19:51324714..51327546,2	MCF-7	breast:
6	chr19:51321294..51329149-chr19:51334672..51341529,13	K562	blood:

Variant related genes	Relation type
KLK1	TF binding region
ENSG00000174562	Chromatin interaction
ENSG00000180279	Chromatin interaction
ENSG00000267968	Chromatin interaction
ENSG00000167747	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1054713	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11672844	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs197589	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1978605	0.90[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2247289	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2411334	0.91[ASN][1000 genomes]
rs2434449	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2456584	0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2456585	0.82[ASN][1000 genomes]
rs2560931	0.82[ASN][1000 genomes]
rs2560933	0.82[ASN][1000 genomes]
rs2560934	0.83[CEU][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2659059	0.83[ASN][1000 genomes]
rs2659099	0.92[ASN][1000 genomes]
rs2659100	0.91[ASN][1000 genomes]
rs2659101	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs2659103	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2659104	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs266114	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs266116	0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs266122	0.82[ASN][1000 genomes]
rs266123	0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs266125	0.82[ASN][1000 genomes]
rs266127	0.82[ASN][1000 genomes]
rs5516	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs788886	0.82[ASN][1000 genomes]
rs788887	0.83[ASN][1000 genomes]
rs788889	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs788890	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs788891	0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060760	chr19:50883425-51463712	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
2	nsv1058177	chr19:50984774-51463712	Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	84 gene(s)	inside rSNPs	diseases
3	nsv912288	chr19:51283791-51334355	Enhancers Bivalent Enhancer Bivalent/Poised TSS Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
4	nsv912289	chr19:51283791-51335943	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
5	nsv912290	chr19:51283791-51344483	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	60 gene(s)	inside rSNPs	diseases
6	nsv526232	chr19:51301230-51335943	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
7	nsv519121	chr19:51308092-51332670	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
8	nsv524637	chr19:51321083-51332670	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv523089	chr19:51321083-51336197	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2659058	KLK1	cis	multi-tissue	Pritchard
rs2659058	KLK1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:51320800-51338800	Weak transcription	Right Atrium	heart
2	chr19:51321800-51327600	Enhancers	Primary B cells from peripheral blood	blood
3	chr19:51324800-51326400	Flanking Active TSS	Pancreas	Pancrea
4	chr19:51324800-51326600	Enhancers	K562	blood
5	chr19:51324800-51327400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr19:51324800-51327800	Enhancers	Duodenum Mucosa	Duodenum
7	chr19:51325200-51326200	Weak transcription	Colonic Mucosa	Colon
8	chr19:51325200-51326800	Weak transcription	Primary B cells from cord blood	blood
9	chr19:51325200-51328000	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr19:51325800-51326600	Bivalent Enhancer	Stomach Mucosa	stomach
11	chr19:51325800-51327600	Enhancers	Fetal Intestine Large	intestine
12	chr19:51326000-51327400	Enhancers	Fetal Intestine Small	intestine
13	chr19:51326000-51327400	Enhancers	Sigmoid Colon	Sigmoid Colon

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